(a) Field of the Invention
The present invention relates to a biochip image analysis system and method thereof. More specifically, the present invention relates to an image analysis system and method for detecting an edge of a cDNA (complementary deoxyribonucleic acid) chip and removing blobs that cause data errors.
(b) Description of the Related Art
Biochips include glass or nylon wafer membranes designed for accelerating genetic research, they are designed for providing a plurality of short DNA strands and essential genetic information for determining living creatures' characteristics on a single substrate, and they are frequently used as test beds for chemical samples.
Biochips may accelerate checking of about 30,000 genes in human DNA, and progression of current global coordinated research thereof, the so-called human genome project, for making a human genome map.
Biochips are classified into protein chips, oligonucleotide chips, and cDNA chips.
Regarding protein chips, dozens to hundreds of different proteins or ligands are provided on the chip surface in a micro-array format. In this instance, when a sample is added to the protein chip, biomolecules specifically interactive with the proteins or ligands provided on the chip surface remain, and others are washed away.
Existence states or functions of the above interactive biomolecules are analyzed using an SPR (surface plasmon resonance) device, a mass spectrometer, or a fluorescence spectrometer. The protein chips may be effectively applied to cancers, AIDS (acquired immune deficiency syndrome), early diagnosis of human diseases, causal examination of diseases, and understanding of in vivo signal transduction systems.
Oligonucleotide chips use 25 oligonucleotides to search for mutations of specified genes. That is, oligonucleotide chips adopt a photolithography method to synthesize oligonucleotides of a desired nucleotide sequence on a slide glass, and they search for mutations of tumor suppressive genes such as p53 and BRCA1 using the synthesized oligonucleotides.
Oligonucleotide chips may be applied to inherited disorder fields including gene mutation detection, drug resistance detection diagnosis, SNP (single nucleotide polymorphism) analysis, histocompatibility and organ transplantation assays, identification of pathogenic microorganisms, nucleotide sequence analysis, paternity tests, interracial polymorphism analysis, and forensic medicine.
As for cDNA chips, thousands to tens of thousands of genes are formed as predetermined-sized spots on a predetermined slide glass substrate to create a cDNA micro-array, fluorescent labeling is performed on mRNAs (messenger ribonucleic acids) of two groups to be compared, that is, the mRNA of a control group and that of an experimental group, and they are competitively combined to the cDNA chip so as to check relative gene expression patterns.
The cDNA micro-array chips generated in this manner contribute greatly to analysis of particular genes expressed in specific cells or tissues. The cDNA micro-array chips may be used for high throughput gene expression—analysis, human disease diagnosis and monitoring, biological response studies of environmental factors, food inspection, new drug development, clinicopathology, and for animal and plant quarantine.
A method for manufacturing the above-noted cDNA micro-array chips will now be described.
Test genes are planted on a glass slide in a spot format having a predetermined size to thereby generate arrays comprising thousands to tens of thousands of spots.
Messenger RNAs are extracted from samples of a control group and an experimental group to perform reverse transcription on the mRNAs, and in this instance, dyes having fluorescence of red Cy5 or green Cy3 are provided to the mRNAs to tag the mRNAs.
In this instance, genes expressed in yellow are provided by superposing green and red, and it is found that similar amounts of the above-noted genes are expressed under the two environments.
The synthesized mRNAs of the two samples are mixed in identical amounts to thus hybridize them on an array chip, uncombined genes are washed from the chip, and hybridized genes remain thereon to generate a cDNA micro-array chip.
The cDNA micro-array chip is read by a laser fluorescent scanner. In this instance, the fluorescent images of the cDNA micro-array chip are scanned by each 5 μm or 10 μm-sized diameter pixel. The fluorescent images are stored in a computer in a 16-bit image format, and fluorescence intensities of the respective genes represent the genes' expression levels, and the levels are analyzed by a computer.
When analyzing cDNA micro-array images, since the cDNA micro-array chip has cDNA of different genes formed as spots of 100 μm˜250 μm diameters that are printed on a glass slide, the respective spots are separated into segments so as to measure expression degrees of the respective genes.
In this instance, a reference circle of a predetermined size is positioned on the center of the segment so as to extract an effective spot, and if the size of the reference circle is greater than that of the spot, the background as well as the spot are positioned within the reference circle, and accordingly, errors occur in data mean values.
In another case, when the center of the spot is not located on the center of the segment but it digresses to a side, since the positions of the reference circle and the spot are not matched, a portion of the spot located in the reference circle is used as effective information, and the remaining spots are processed as a background to thereby increase data error rates.
Blobs or streaks are generated on the segments of the cDNA micro-array chip because of artifacts or other factors provided from the outside, and the blobs or streaks change the mean value and the standard deviation of the intensity of the spots or the background because of the very high intensities of the blobs, and accordingly, if the blobs are not removed, erroneous data may be obtained.
Further, since the images obtained by a scanning process via the fluorescent scanner and other types of images generated from various converting and analyzing processes occupy a very large part of the memory capacity, the time spent for outputting desired images on a screen or analyzing data may be very much longer.